LiRA - WG1 Vector non EU from EFSA Systematic literature review
Alfredo Acosta SVA
2024-07-04
1 Analisis of efsa publication on vectors
- Systematic literature review on the vector status of potential vector species of 36 vector-borne pathogens
- Information needed for the integration of WG1-WG2
# Library ----
library(readxl)
library(dplyr)##
## Attaching package: 'dplyr'## The following objects are masked from 'package:stats':
##
## filter, lag## The following objects are masked from 'package:base':
##
## intersect, setdiff, setequal, unionlibrary(lubridate)##
## Attaching package: 'lubridate'## The following objects are masked from 'package:base':
##
## date, intersect, setdiff, unionlibrary(leaflet)
library(sf)## Linking to GEOS 3.11.2, GDAL 3.7.2, PROJ 9.3.0; sf_use_s2() is TRUElibrary(DT)
library(ggplot2)setwd("C:/Users/alfredo.acosta/OneDrive - SVA/LORA/Working example/vectors/")2 DB EfSA
2.1 Reading data
w <- read_xlsx("DL3.1.2.SLR_VectorStatus_Database_comp.xlsx", sheet = 1)3 Contents of the DB
colnames(w)## [1] "ID" "First_Author" "Title"
## [4] "year" "Country" "Region/State"
## [7] "City/County" "Latitude" "Longitude"
## [10] "Continent" "Year_Start" "Year_End"
## [13] "Month_Start" "Month_End" "Continuous_or_annually"
## [16] "SamplingMethod" "LifeStage" "VectorGroup"
## [19] "VectorSpecies" "VectorSpeciesOld" "fedStatus"
## [22] "Host" "anMethCode" "MethodCategory"
## [25] "NÂSpecimensÂTested" "NPoolsTested" "Pool_size"
## [28] "Positive/Negative" "NPoolspositive" "VBD_Agent"
## [31] "VBD_Agent_subtype" "VBD_AS_Full" "MIR"
## [34] "LCI_MIR" "UCI_MIR" "Vectornet_Region"
## [37] "Trap/Host" "PrioritySpecies" "VectornetRegionSpecies"
## [40] "Vndatlocd" "Vnmaplocd" "Country_ISO"table(w$year)##
## 1973 1989 1998 1999 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011
## 3 167 4 4 49 134 22 49 58 31 103 395 64 98 78 63
## 2012 2013 2014 2015 2016 2017 2018 2019 2020 2021 2022 2023
## 112 113 302 298 337 791 653 370 376 657 383 13table(w$Continent)##
## Africa Eurasia Eurasia, Africa North America Oceania
## 902 2914 14 1333 250
## South America
## 311table(w$Host)##
## (caught in cow shed)
## 24
## American Robin
## 2
## Anatolian wild sheep
## 4
## Ardea herodius
## 1
## Baltimore Oriole
## 1
## bird
## 24
## bird, dog, human, pig
## 1
## Birds
## 6
## Black-capped chikadee
## 1
## bloodfed?
## 1
## Bos taurus
## 5
## bovine
## 2
## Bovine
## 1
## bovine, dog
## 1
## Bovine, Dog, barking deer, wild boar, leopard
## 1
## bovine, dog, sambar deer, civet
## 1
## bovine, goat, dog,sambar deer, civet
## 1
## Bubulcus ibis
## 1
## Buffalo
## 1
## bull
## 4
## camel
## 10
## Camel
## 3
## camels
## 16
## Camelus dromedarius
## 8
## Canis lupus
## 2
## Canis lupus domesticus
## 4
## Canis lupus familiaris
## 29
## Capra hircus
## 12
## Capreolus capreolus
## 1
## cat
## 2
## Cat
## 2
## cattle
## 163
## Cattle
## 23
## cattle (freshly slaughtered)
## 26
## cattle and goat
## 2
## cattle and pigs
## 3
## cattle and sheep
## 7
## cattle, domestic and roving dogs, smalls mammals
## 25
## Cattle, goats
## 2
## Cattle, goats, sheep
## 4
## Cattle, goats, sheep, dogs
## 7
## Cattle, goats, sheep, tortoises
## 1
## cattle, Lepus europaeus, questing ticks
## 2
## cattle, ruminants, horeses
## 2
## Cattle, sheep
## 20
## cattle, sheep, goat
## 6
## cattle, sheep, goats
## 28
## cattle, sheep, horse, Lepus europaeus, man, questing ticks, Lepus europaeus, Corvus frugilegus, Galerida cristata
## 2
## Cattle, tortoises
## 1
## cattles
## 3
## Cervus elaphus hispanicus
## 3
## Chickens
## 1
## Chrysocyon brachyurus
## 1
## Common Yellowthroat
## 2
## cow
## 7
## Cow
## 12
## cow, dog, pig
## 1
## cow, dog, sheep, pig
## 1
## cow, sheep, goat
## 6
## crow
## 1
## deer
## 30
## deer, boar
## 1
## dog
## 19
## Dog
## 9
## Dog, sheep
## 2
## Dog, sheep, goats
## 2
## dogs
## 2
## dogs, cats, horses
## 218
## domestic ruminants
## 1
## donkey
## 1
## Donkey, goat, camel and others
## 1
## Eastern Towhee
## 1
## Ergretta thula
## 1
## fallow deer
## 3
## Farm animals
## 1
## Felis catus
## 1
## flagging, dog, hedgehog, european badger, tortoise
## 3
## fox
## 1
## goat
## 18
## Goat
## 10
## goat, sheep
## 21
## Goat, sheep
## 1
## goats
## 8
## goats, sheep, cattle, buffalo
## 8
## greek tortoise, camels
## 2
## ground squirrel
## 1
## Guinea fowls
## 2
## hare
## 5
## Hares
## 1
## hedgehog
## 4
## Homo sapiens
## 15
## House Wren
## 1
## human
## 17
## Human
## 8
## human, bird
## 1
## Human, cattle, sheep, goat, unidentified and others
## 1
## Hydrochoerus hydrochaeris
## 1
## Indigo Bunting
## 1
## Indotestudo elongata
## 2
## Lincoln's Sparrow
## 1
## livestock, sheep
## 4
## lon-legged buzzard
## 1
## Meles meles
## 1
## Migratory birds
## 2
## Monitor lizards
## 1
## mouflon, wild boar
## 1
## NA
## 2464
## None
## 19
## North American porcupine
## 1
## Northern Waterthrush
## 1
## Ovenbird
## 1
## Ovis aries
## 5
## ox
## 32
## partridge
## 1
## Passer domesticus
## 1
## Pelecanus erythrorhunchos
## 1
## pig, dog, human, sheep
## 1
## Poultry
## 1
## python
## 1
## questing tick
## 3
## red deer
## 2
## Red deer and wild boar
## 2
## red deer, wild boar
## 2
## sambar deer
## 2
## shee
## 1
## sheep
## 66
## Sheep
## 37
## Sheep, bovine
## 2
## sheep, cattle
## 1
## sheep, cattle, goat
## 5
## sheep, cattle, goats
## 5
## sheep, goat
## 8
## Sheep, goat
## 1
## Sheep, goat, unidentified
## 1
## sheep, humans
## 1
## Sika deer
## 4
## Song Sparrow
## 1
## Sus scrofa
## 2
## Testudo graeca
## 1
## tortoise
## 2
## Tortoises
## 2
## Turdus migratorius
## 1
## Turkey
## 1
## unclear
## 815
## Urctos arsos
## 1
## Veery
## 1
## Vulpes vulpes
## 7
## warthog burrows
## 5
## wild boar
## 6
## Wild boar
## 9
## yellow legged gulls
## 1table(w$VBD_AS_Full)##
## African horse sickness virus African swine fever virus
## 27 239
## Akabane virus Alkhurma haemorrhagic fever virus
## 21 13
## Bluetongue virus Cache Valley virus
## 266 120
## Crimean-Congo haemorrhagic fever virus Eastern equine encephalitis virus
## 637 118
## Ehrlichia ruminantium Epizootic hemorrhagic disease virus
## 197 79
## Equine encephalosis virus Getah virus
## 20 44
## Hepatozoon canis Japanese encephalitis virus
## 534 437
## Leishmania infantum Rift Valley fever virus
## 567 101
## Schmallenberg virus Shuni virus
## 262 10
## St. Louis encephalitis virus Thogoto virus
## 46 1
## Venezuelan equine encephalitis virus Vesicular stomatitis - Indiana virus
## 10 13
## Wesselsbron virus West Nile virus
## 6 1927
## Western equine encephalitis virus Yunnan orbivirus
## 12 20table(w$VBD_Agent_subtype)##
## AHFV AHSV AKAV ASFV BTV CanL CCHFV cowdr Cowdr CVV EEEV EEV EHDV
## 13 27 21 239 266 567 637 23 174 120 118 20 79
## GETV hepat JEV RVFV SBV SHUV SLEV THOV VEEV VSIV WEEV WNV WSLV
## 44 534 437 101 262 10 46 1 10 13 12 1927 6
## YUOV
## 20table(w$VBD_Agent_subtype)##
## AHFV AHSV AKAV ASFV BTV CanL CCHFV cowdr Cowdr CVV EEEV EEV EHDV
## 13 27 21 239 266 567 637 23 174 120 118 20 79
## GETV hepat JEV RVFV SBV SHUV SLEV THOV VEEV VSIV WEEV WNV WSLV
## 44 534 437 101 262 10 46 1 10 13 12 1927 6
## YUOV
## 20table(w$VectorGroup)##
## Biting midges mosquitoes Mosquitoes Sand flies Ticks
## 715 6 2813 557 1636table(w$VectorSpecies)##
## Aedeomyia furfurea
## 3
## Aedeomyia madagascarica
## 3
## Aedeomyia squamipennis
## 2
## Aedes abserratus
## 6
## Aedes abserratus/punctor
## 2
## Aedes aegypti
## 21
## Aedes albodorsalis
## 1
## Aedes albolateralis
## 1
## Aedes albopictus
## 134
## Aedes albothorax
## 1
## Aedes andamanensis
## 1
## Aedes annandalei
## 6
## Aedes annulipes
## 3
## Aedes argenteopunctatus
## 1
## Aedes atlanticus
## 2
## Aedes atlanticus/tormentor
## 3
## Aedes atropalpus
## 1
## Aedes aurifer
## 6
## Aedes caballus
## 2
## Aedes canadensis
## 19
## Aedes cantans
## 7
## Aedes cantator
## 14
## Aedes caspius
## 92
## Aedes cinereus
## 29
## Aedes cinereus/geminus
## 6
## Aedes circumluteolus
## 3
## Aedes communis
## 6
## Aedes communis group
## 2
## Aedes culiciformis
## 1
## Aedes cumminsii
## 4
## Aedes dalzieli
## 3
## Aedes dentatus
## 2
## Aedes detritus
## 8
## Aedes domesticus
## 1
## Aedes dorsalis
## 10
## Aedes durbanensis
## 2
## Aedes excrucians
## 8
## Aedes fitchii
## 2
## Aedes flavescens
## 5
## Aedes fulvus pallens
## 1
## Aedes furcifer
## 1
## Aedes geniculata
## 3
## Aedes geniculatus
## 14
## Aedes gibbinsi
## 4
## Aedes grossbecki
## 3
## Aedes hendersoni
## 2
## Aedes hirsutus
## 1
## Aedes increpitus
## 1
## Aedes ingrami
## 2
## Aedes intrudens
## 2
## Aedes japonicus
## 28
## Aedes katherinensis
## 1
## Aedes kochi
## 1
## Aedes koreicus
## 2
## Aedes littlechildi
## 1
## Aedes luteocephalus
## 1
## Aedes maculipennis
## 3
## Aedes mcintoshi
## 2
## Aedes mediovittatus
## 1
## Aedes melanimon
## 3
## Aedes metallicus
## 1
## Aedes minimus
## 3
## Aedes nigromaculis
## 1
## Aedes notoscriptus
## 2
## Aedes ochraceus
## 6
## Aedes penghuensis
## 2
## Aedes phylolabis
## 1
## Aedes pulcritarsis
## 2
## Aedes rossicus
## 6
## Aedes rusticus
## 1
## Aedes scapularis
## 2
## Aedes scutellaris
## 1
## Aedes serratus
## 1
## Aedes simpsoni
## 1
## Aedes sollicitans
## 18
## Aedes spenceri
## 1
## Aedes sticticus
## 13
## Aedes stimulans
## 14
## Aedes stimulans group
## 4
## Aedes stoneorum
## 1
## Aedes subargenteus
## 1
## Aedes sudanensis
## 1
## Aedes taeniorhynchus
## 20
## Aedes tarsalis
## 1
## Aedes thibaulti
## 4
## Aedes togoi
## 2
## Aedes tortilis
## 1
## Aedes tremulus
## 1
## Aedes tricholabis
## 6
## Aedes trichuris
## 2
## Aedes triseriatus
## 33
## Aedes triseriatus/hendersoni
## 1
## Aedes trivittatus
## 24
## Aedes vexans
## 93
## Aedes vexans arabiensis
## 6
## Aedes vexans nipponii
## 1
## Aedes vexans nocturnus
## 1
## Aedes vexans s.l.
## 1
## Aedes vigilax
## 1
## Aedes vittatus
## 1
## Amblyomma brasiliense
## 1
## Amblyomma cajennense
## 2
## Amblyomma cohaerens
## 3
## Amblyomma detritum
## 2
## Amblyomma dubitatum
## 2
## Amblyomma falsomarmoreum
## 1
## Amblyomma gemma
## 6
## Amblyomma geoemydae
## 2
## Amblyomma gervaisi
## 1
## Amblyomma hebraeum
## 42
## Amblyomma integrum
## 1
## Amblyomma latum
## 1
## Amblyomma lepidum
## 7
## Amblyomma marmoreum
## 2
## Amblyomma nutalli
## 1
## Amblyomma parvum
## 1
## Amblyomma sculptum
## 2
## Amblyomma sparsum
## 1
## Amblyomma testudinarium
## 8
## Amblyomma tigrinum
## 1
## Amblyomma triguttatum triguttatum
## 11
## Amblyomma variegatum
## 101
## Anopheles albimanus
## 2
## Anopheles algeriensis
## 2
## Anopheles annulipes
## 1
## Anopheles apoci
## 1
## Anopheles aquasalis
## 2
## Anopheles atroparvus
## 2
## Anopheles atropos
## 5
## Anopheles barberi
## 7
## Anopheles barbirostris
## 4
## Anopheles claviger
## 11
## Anopheles claviger/petragnani
## 4
## Anopheles coustani
## 6
## Anopheles crucians
## 9
## Anopheles crucians s.l.
## 2
## Anopheles dthali
## 2
## Anopheles farauti s.l.
## 1
## Anopheles fluviatilis
## 2
## Anopheles franciscanus
## 4
## Anopheles freeborni
## 4
## Anopheles funestus
## 4
## Anopheles gambiae
## 6
## Anopheles grabhamii
## 1
## Anopheles hermsi
## 2
## Anopheles hilli
## 1
## Anopheles hyrcanus
## 6
## Anopheles implexus
## 3
## Anopheles kochi
## 3
## Anopheles kunmingensis
## 3
## Anopheles ludlowae
## 1
## Anopheles maculipalpis
## 2
## Anopheles maculipennis
## 31
## Anopheles maculipennis group
## 2
## Anopheles maculipennis s.l.
## 21
## Anopheles marteri
## 1
## Anopheles mascarensis
## 1
## Anopheles messeae
## 3
## Anopheles minimus
## 3
## Anopheles multicolor
## 1
## Anopheles neomaculipalpus
## 2
## Anopheles pauliani
## 3
## Anopheles peditaeniatus
## 3
## Anopheles pharoensis
## 6
## Anopheles plumbeus
## 15
## Anopheles pseudopictus
## 3
## Anopheles punctipennis
## 23
## Anopheles quadrimaculatus
## 28
## Anopheles quadrimaculatus s.l.
## 2
## Anopheles rufipes
## 7
## Anopheles sacharovi
## 1
## Anopheles sergentii
## 1
## Anopheles sinensis
## 18
## Anopheles squamosus
## 2
## Anopheles squamosus/cydippis
## 3
## Anopheles stephensi
## 2
## Anopheles subpictus
## 22
## Anopheles superpictus
## 4
## Anopheles tenebrosus
## 3
## Anopheles tessellatus
## 9
## Anopheles vagus
## 4
## Anopheles vestitipennis
## 2
## Anopheles walkeri
## 11
## Anopheles ziemanni
## 1
## Argas persicus
## 2
## Argas reflexus
## 1
## Argas vulgaris
## 2
## Armigeres subalbatus
## 17
## Bichromomyia flaviscutellata
## 4
## Bichromomyia olmeca olmeca
## 3
## Boophilus annulatus
## 3
## Boophilus decoratus
## 1
## Brumptomyia avellari
## 2
## Brumptomyia hamata
## 1
## Brumptomyia mesai
## 1
## Brumptomyia nitzulescui
## 1
## Coquillettidia aurites
## 3
## Coquillettidia crassipes
## 3
## Coquillettidia fraseri
## 1
## Coquillettidia fuscopennata
## 3
## Coquillettidia metallica
## 4
## Coquillettidia nigricans
## 1
## Coquillettidia ochracea
## 2
## Coquillettidia Ochracea
## 1
## Coquillettidia perturbans
## 35
## Coquillettidia pseudoconopas
## 1
## Coquillettidia richiardii
## 17
## Coquillettidia venezuelensis
## 1
## Coquillettidia versicolor
## 2
## Culex adersianus
## 1
## Culex annulatus
## 1
## Culex annulioris
## 4
## Culex annulus
## 16
## Culex antennatus
## 12
## Culex atratus
## 2
## Culex bahamensis
## 2
## Culex bidens/interfor
## 1
## Culex bitaeniorhynchus
## 13
## Culex boharti
## 1
## Culex brevipalpis
## 1
## Culex cedecei
## 2
## Culex chidesteri
## 1
## Culex coronator
## 2
## Culex decens
## 5
## Culex duttoni
## 1
## Culex erraticus
## 23
## Culex erythrothorax
## 17
## Culex fuscanus
## 3
## Culex fuscocephala
## 22
## Culex gelidus
## 23
## Culex habilitator
## 1
## Culex hortensis
## 5
## Culex impudicus
## 2
## Culex inatomii
## 1
## Culex infula
## 2
## Culex interrogator
## 1
## Culex iolambdis
## 1
## Culex janitor
## 1
## Culex laticinctus
## 1
## Culex martinii
## 2
## Culex mimeticus
## 5
## Culex modestus
## 32
## Culex murrelli
## 3
## Culex neavei
## 10
## Culex nebulosus
## 1
## Culex nigripalpus
## 13
## Culex nigropunctatus
## 1
## Culex opisthopus
## 1
## Culex orientalis
## 2
## Culex pedroi
## 1
## Culex perexiguus
## 9
## Culex perfuscus
## 4
## Culex pipiens
## 317
## Culex pipiens biotype molestus
## 2
## Culex pipiens biotype pipiens
## 7
## Culex pipiens biotype pipiens x Culex pipiens biotype molestus
## 1
## Culex pipiens pallens
## 4
## Culex pipiens s.l.
## 65
## Culex pipiens x Culex quinquefasciatus
## 5
## Culex pipiens/restuans
## 47
## Culex pipiens/torrentium
## 2
## Culex poicilipes
## 13
## Culex pseudovishnui
## 17
## Culex pusillus
## 2
## Culex quinquefasciatus
## 105
## Culex restuans
## 55
## Culex rima
## 1
## Culex rubinotus
## 1
## Culex rubithoracis
## 5
## Culex salinarius
## 31
## Culex simpsoni
## 1
## Culex sinensis
## 1
## Culex sitiens
## 4
## Culex sitiens group
## 3
## Culex sitiens subgroup
## 8
## Culex spinosus
## 1
## Culex stigmatosoma
## 6
## Culex striatipes
## 1
## Culex taeniopus
## 1
## Culex tarsalis
## 90
## Culex territans
## 28
## Culex terzii
## 1
## Culex theileri
## 26
## Culex thriambus
## 6
## Culex tigripes
## 1
## Culex torrentium
## 3
## Culex trifilatus
## 2
## Culex tritaeniorhynchus
## 148
## Culex univittatus
## 16
## Culex vagans
## 3
## Culex vansomereni
## 1
## Culex vicinus
## 1
## Culex vishnui
## 19
## Culex vishnui subgroup
## 2
## Culex watti
## 1
## Culex whitmorei
## 11
## Culex zombaensis
## 2
## Culicoides achrayi
## 4
## Culicoides actoni
## 2
## Culicoides alazanicus
## 2
## Culicoides arakawae
## 10
## Culicoides arakawai
## 1
## Culicoides arboricola
## 4
## Culicoides badooshennis
## 1
## Culicoides baueri
## 2
## Culicoides begueti
## 1
## Culicoides bickleyi
## 1
## Culicoides biguttatus
## 2
## Culicoides brunnicans
## 1
## Culicoides cataneii/gejgelensis
## 2
## Culicoides chiopterus
## 16
## Culicoides circumscriptus
## 7
## Culicoides clastrieri
## 2
## Culicoides crepuscularis
## 11
## Culicoides cylindratus
## 2
## Culicoides debilipalpis
## 12
## Culicoides deltus
## 2
## Culicoides dendriticus
## 1
## Culicoides dewulfi
## 22
## Culicoides duddingstoni
## 1
## Culicoides fagineus
## 2
## Culicoides fascipennis
## 3
## Culicoides festivipennis
## 6
## Culicoides flavipulicaris
## 7
## Culicoides fulvus
## 4
## Culicoides furcillatus
## 1
## Culicoides furens
## 1
## Culicoides gejgelensis
## 2
## Culicoides griseidorsum
## 1
## Culicoides grisescens
## 1
## Culicoides guttifer
## 1
## Culicoides guttipennis
## 2
## Culicoides haematopotus
## 12
## Culicoides haranti
## 1
## Culicoides heliophilus
## 1
## Culicoides hinmani
## 1
## Culicoides homotomus
## 4
## Culicoides humeralis
## 2
## Culicoides imicola
## 43
## Culicoides imicola s.l.
## 3
## Culicoides imicola/bolitinos
## 1
## Culicoides impunctatus
## 2
## Culicoides insignipennis
## 1
## Culicoides insignis
## 4
## Culicoides jacobsoni
## 3
## Culicoides kibunensis
## 1
## Culicoides liui
## 1
## Culicoides longipennis
## 3
## Culicoides lungchiensis
## 2
## Culicoides lupicaris
## 2
## Culicoides maritimus
## 3
## Culicoides matsuzawai
## 2
## Culicoides minutissimus
## 1
## Culicoides mississippiensis
## 1
## Culicoides nanus
## 2
## Culicoides newsteadi
## 31
## Culicoides newsteadi complex
## 2
## Culicoides newsteadi group
## 4
## Culicoides newsteadi s.l.
## 1
## Culicoides nipponensis
## 20
## Culicoides nubeculosus
## 6
## Culicoides nubeculosus s.l.
## 14
## Culicoides obsoletus complex
## 103
## Culicoides obsoletus group
## 10
## Culicoides obsoletus s.l.
## 24
## Culicoides obsoletus/sanguisuga
## 1
## Culicoides odiatus
## 1
## Culicoides odibilis
## 1
## Culicoides ohmorii
## 2
## Culicoides orientalis
## 15
## Culicoides oxystoma
## 26
## Culicoides pallidicornis
## 2
## Culicoides paolae
## 1
## Culicoides paraensis
## 1
## Culicoides parroti
## 2
## Culicoides peregrinus
## 11
## Culicoides pictipennis
## 1
## Culicoides picturatus
## 1
## Culicoides poperinghensis
## 1
## Culicoides pulicaris
## 44
## Culicoides pulicaris group
## 7
## Culicoides pulicaris s.l.
## 21
## Culicoides pulicaris/lupicaris
## 1
## Culicoides punctatus
## 43
## Culicoides puncticollis
## 3
## Culicoides pusillus
## 2
## Culicoides reconditus
## 1
## Culicoides riethi
## 1
## Culicoides riouxi
## 1
## Culicoides salinarius
## 2
## Culicoides santonicus
## 1
## Culicoides scanloni
## 1
## Culicoides schultzei s.l.
## 3
## Culicoides scoticus
## 4
## Culicoides segnis
## 1
## Culicoides sejfadinei/tauricus
## 1
## Culicoides shaklawensis
## 1
## Culicoides simulator
## 1
## Culicoides sonorensis
## 11
## Culicoides spiculae
## 1
## Culicoides spinosus
## 3
## Culicoides stellifer
## 14
## Culicoides stigma
## 1
## Culicoides subfagineus
## 1
## Culicoides subfasciipennis
## 3
## Culicoides sumatrae
## 2
## Culicoides tagineus
## 1
## Culicoides tainanus
## 4
## Culicoides torreyae
## 1
## Culicoides venustus
## 13
## Culicoides vexans
## 1
## Culicoides villosipennis
## 2
## Culiseta alaskaensis
## 1
## Culiseta annulata
## 23
## Culiseta impatiens
## 1
## Culiseta incidens
## 7
## Culiseta inornata
## 16
## Culiseta longiareolata
## 24
## Culiseta melanura
## 70
## Culiseta minnesotae
## 6
## Culiseta morsitans
## 7
## Culiseta particeps
## 1
## Culiseta subochrea
## 3
## Dampfomyia beltrani
## 4
## Deinocerites cancer
## 3
## Deinocerites magnus
## 1
## Dermacentor auratus
## 1
## Dermacentor marginatus
## 44
## Dermacentor niveus
## 3
## Dermacentor nuttalli
## 4
## Dermacentor raskenmensis
## 1
## Dermacentor reticulatus
## 11
## Dermacentor silvarum
## 2
## Evandromyia bacula
## 1
## Evandromyia bourrouli
## 1
## Evandromyia carmelinoi
## 4
## Evandromyia cortelezii
## 7
## Evandromyia cortelezii s.l.
## 3
## Evandromyia edwardsi
## 3
## Evandromyia evandroi
## 4
## Evandromyia lenti
## 8
## Evandromyia sallesi
## 4
## Evandromyia saulensis
## 1
## Evandromyia spelunca
## 1
## Evandromyia teratodes
## 1
## Evandromyia termitophila
## 6
## Evandromyia walkeri
## 4
## Expapillata firmatoi
## 1
## Haemagogus mesodentatus
## 1
## Haemaphysalis adleri
## 1
## Haemaphysalis bancrofti
## 4
## Haemaphysalis bispinosa
## 2
## Haemaphysalis concinna
## 8
## Haemaphysalis erinacei
## 8
## Haemaphysalis flava
## 6
## Haemaphysalis formosensis
## 6
## Haemaphysalis hystricis
## 3
## Haemaphysalis inermis
## 6
## Haemaphysalis intermedia
## 1
## Haemaphysalis kitaokai
## 3
## Haemaphysalis lagostrophi
## 1
## Haemaphysalis leachi
## 2
## Haemaphysalis longicornis
## 31
## Haemaphysalis parva
## 27
## Haemaphysalis punctata
## 22
## Haemaphysalis qinghaiensis
## 1
## Haemaphysalis shimoga
## 1
## Haemaphysalis spinigera
## 1
## Haemaphysalis sulcata
## 21
## Hyalomma aegyptium
## 15
## Hyalomma anatolicum
## 55
## Hyalomma anatolicum anatolicum
## 1
## Hyalomma asiaticum
## 29
## Hyalomma asiaticum asiaticum
## 3
## Hyalomma detritum
## 9
## Hyalomma dromedarii
## 34
## Hyalomma excavatum
## 28
## Hyalomma glabrum
## 1
## Hyalomma impeltatum
## 9
## Hyalomma impressum
## 4
## Hyalomma lusitanicum
## 36
## Hyalomma marginatum
## 86
## Hyalomma marginatum rufipes
## 2
## Hyalomma marmoreum
## 2
## Hyalomma rufipes
## 12
## Hyalomma rufipes truncatum
## 1
## Hyalomma schulzei
## 3
## Hyalomma scupense
## 14
## Hyalomma truncatum
## 16
## Hyalomma turanicum
## 2
## Ixodes cornuatus
## 5
## Ixodes crenulatus
## 2
## Ixodes frontalis
## 2
## Ixodes gibbosus
## 1
## Ixodes hexagonus
## 4
## Ixodes hirsti
## 1
## Ixodes holocyclus
## 84
## Ixodes inopinatus
## 2
## Ixodes laguri
## 1
## Ixodes myrmecobii
## 2
## Ixodes nipponensis
## 1
## Ixodes ovatus
## 1
## Ixodes pavlovskyi
## 3
## Ixodes persulcatus
## 6
## Ixodes redikorzevi
## 1
## Ixodes ricinus
## 46
## Ixodes scapularis
## 22
## Ixodes tasmani
## 18
## Ixodes turdus
## 1
## Ixodes ventalloi
## 2
## Lutzia tigripes
## 2
## Lutzomyia almerioi
## 3
## Lutzomyia antunesi
## 1
## Lutzomyia cavernicola
## 2
## Lutzomyia cortelezzii s.l.
## 1
## Lutzomyia cruciata
## 5
## Lutzomyia cruzi
## 1
## Lutzomyia edwardsi
## 1
## Lutzomyia evandroi
## 1
## Lutzomyia firmatoi
## 1
## Lutzomyia fischeri
## 1
## Lutzomyia flaviscutellata
## 2
## Lutzomyia forattinii
## 1
## Lutzomyia gaminarai
## 1
## Lutzomyia gomezi
## 1
## Lutzomyia intermedia
## 1
## Lutzomyia lenti
## 1
## Lutzomyia lloydi
## 1
## Lutzomyia longipalpis
## 82
## Lutzomyia Longipalpis
## 9
## Lutzomyia migonei
## 2
## Lutzomyia neivai
## 1
## Lutzomyia renei
## 1
## Lutzomyia sordellii
## 1
## Lutzomyia tupynambai
## 1
## Lutzomyia ubiquitalis
## 1
## Lutzomyia umbratilis
## 1
## Lutzomyia wellcomei
## 1
## Lutzomyia whitmani
## 5
## Mansonia africana
## 3
## Mansonia annulifera
## 1
## Mansonia bonneae
## 1
## Mansonia dives
## 2
## Mansonia dyari/titillans
## 1
## Mansonia flaveola
## 1
## Mansonia indiana
## 2
## Mansonia nigerrima
## 3
## Mansonia titillans
## 5
## Mansonia uniformis
## 24
## Margaropus winthemi
## 1
## Martinsmyia minasensis
## 1
## Martinsmyia oliveirai
## 2
## Micropygomyia cayennensis cayennensis
## 2
## Micropygomyia chiapanensis
## 1
## Micropygomyia echinatopharynx
## 1
## Micropygomyia quinquefer
## 5
## Micropygomyia rorotaensis
## 1
## Micropygomyia villelai
## 1
## Migonemyia migonei
## 7
## Mimomyia luzonensis
## 1
## Mimomyia splendens
## 2
## Nyssomyia intermedia
## 2
## Nyssomyia Intermedia
## 1
## Nyssomyia neivai
## 3
## Nyssomyia whitmani
## 16
## Nyssomyia yuilli yuilli
## 1
## Ornithodoros canestrinii
## 1
## Ornithodoros compactus
## 2
## Ornithodoros kalahariensis
## 1
## Ornithodoros maritimus
## 2
## Ornithodoros moubata
## 3
## Ornithodoros moubata s.l.
## 177
## Ornithodoros noorsveldensis
## 1
## Ornithodoros phacochoerus
## 2
## Ornithodoros porcinus
## 12
## Ornithodoros porcinus domesticus
## 6
## Ornithodoros porcinus porcinus
## 8
## Ornithodoros waterbergensis
## 1
## Ornithodoros zumpti
## 1
## Orthopodomyia alba
## 1
## Orthopodomyia signifera
## 5
## Phlebotomus alexandri
## 8
## Phlebotomus anatolicus
## 1
## Phlebotomus argentipes
## 24
## Phlebotomus ariasi
## 5
## Phlebotomus balcanicus
## 2
## Phlebotomus brevis
## 1
## Phlebotomus chabaudi
## 2
## Phlebotomus duboscqi
## 1
## Phlebotomus halepensis
## 2
## Phlebotomus jacusieli
## 2
## Phlebotomus kandelakii
## 2
## Phlebotomus killicki
## 1
## Phlebotomus langeroni
## 1
## Phlebotomus longicuspis
## 10
## Phlebotomus major s.l.
## 6
## Phlebotomus mascittii
## 4
## Phlebotomus neglectus
## 10
## Phlebotomus neglectus/syriacus
## 1
## Phlebotomus papatasi
## 52
## Phlebotomus perfiliewi
## 13
## Phlebotomus perniciosus
## 36
## Phlebotomus rodhaini
## 1
## Phlebotomus sergenti
## 10
## Phlebotomus simici
## 2
## Phlebotomus simici/halepensis
## 1
## Phlebotomus similis
## 1
## Phlebotomus tobbi
## 12
## Phlebotomus wenyoni
## 2
## Pintomyia christenseni
## 4
## Pintomyia evansi
## 2
## Pintomyia fischeri
## 4
## Pintomyia misionensis
## 1
## Pintomyia monticola
## 4
## Pintomyia ovallesi
## 1
## Pintomyia pessoai
## 3
## Pressatia choti
## 1
## Psathyromyia aclydifera
## 6
## Psathyromyia aragaoi
## 1
## Psathyromyia baratai
## 1
## Psathyromyia bigeniculata
## 2
## Psathyromyia campograndensis
## 1
## Psathyromyia carpenteri
## 5
## Psathyromyia hermanlenti
## 2
## Psathyromyia lanei
## 2
## Psathyromyia lutziana
## 3
## Psathyromyia shannoni
## 3
## Psathyromyia undulata
## 1
## Psorophora albigenu
## 1
## Psorophora ciliata
## 3
## Psorophora columbiae
## 6
## Psorophora confinnis
## 2
## Psorophora cyanescens
## 1
## Psorophora ferox
## 22
## Psorophora howardii
## 2
## Psychodopygus Brasiliensis
## 1
## Psychodopygus davisi
## 2
## Psychodopygus Lutziana
## 1
## Psychodopygus panamensis
## 6
## Rhipicephalus annulatus
## 17
## Rhipicephalus appendiculatus
## 13
## Rhipicephalus australis
## 2
## Rhipicephalus bursa
## 44
## Rhipicephalus camicasi
## 2
## Rhipicephalus decoloratus
## 28
## Rhipicephalus evertsi
## 12
## Rhipicephalus evertsi evertsi
## 4
## Rhipicephalus geigyi
## 8
## Rhipicephalus guilhoni
## 1
## Rhipicephalus haemaphysaloides
## 1
## Rhipicephalus microplus
## 16
## Rhipicephalus muhsamae
## 1
## Rhipicephalus praetextatus
## 2
## Rhipicephalus pravus
## 2
## Rhipicephalus pulchellus
## 5
## Rhipicephalus pumilio
## 2
## Rhipicephalus rossicus
## 5
## Rhipicephalus sanguineus
## 168
## Rhipicephalus sanguineus group
## 2
## Rhipicephalus sanguineus s.l.
## 40
## Rhipicephalus schulzei
## 1
## Rhipicephalus senegalensis
## 4
## Rhipicephalus simpsoni
## 1
## Rhipicephalus turanicus
## 41
## Sciopemyia microps
## 1
## Sciopemyia sordellii
## 8
## Sergentomyia alderi
## 1
## Sergentomyia antennata
## 3
## Sergentomyia buxtoni
## 1
## Sergentomyia clydei
## 1
## Sergentomyia dentata
## 5
## Sergentomyia dreyfussi
## 2
## Sergentomyia dubia
## 1
## Sergentomyia fallax
## 2
## Sergentomyia magna
## 1
## Sergentomyia minuta
## 20
## Sergentomyia schwetzi
## 1
## Trichopygomyia longispina
## 1
## Uranotaenia balfouri
## 1
## Uranotaenia cooki
## 1
## Uranotaenia lowii
## 1
## Uranotaenia macfarlanei
## 1
## Uranotaenia sapphirina
## 18
## Uranotaenia unguiculata
## 6
## Verrallina carmenti
## 1
## Verrallina funerea
## 1
## Wyeomyia mitchellii
## 2length(unique(w$VectorSpecies))## [1] 687head(w)## # A tibble: 6 × 42
## ID First_Author Title year Country `Region/State` `City/County` Latitude
## <chr> <chr> <chr> <dbl> <chr> <chr> <chr> <chr>
## 1 2 Li Invest… 2017 China Yunnan provin… <NA> "Sampli…
## 2 2 Li Invest… 2017 China Yunnan provin… <NA> "Sampli…
## 3 2 Li Invest… 2017 China Yunnan provin… <NA> "Sampli…
## 4 2 Li Invest… 2017 China Yunnan provin… <NA> "Sampli…
## 5 2 Li Invest… 2017 China Yunnan provin… <NA> "Sampli…
## 6 2 Li Invest… 2017 China Yunnan provin… <NA> "Sampli…
## # ℹ 34 more variables: Longitude <dbl>, Continent <chr>, Year_Start <chr>,
## # Year_End <chr>, Month_Start <chr>, Month_End <chr>,
## # Continuous_or_annually <chr>, SamplingMethod <chr>, LifeStage <chr>,
## # VectorGroup <chr>, VectorSpecies <chr>, VectorSpeciesOld <chr>,
## # fedStatus <chr>, Host <chr>, anMethCode <chr>, MethodCategory <chr>,
## # `NÂSpecimensÂTested` <dbl>, NPoolsTested <dbl>, Pool_size <chr>,
## # `Positive/Negative` <chr>, NPoolspositive <chr>, VBD_Agent <chr>, …4 Species specified on the Vector net output
species <- c("Aedes albopictus",
"Aedes vexans vexans",
"Aedes aegypti",
"Aedes japonicus",
"Culex pipiens",
"Culex modestus", #MC: 28.11.2023 added
"Culex tarsalis", ## not in the dataset
"Culex quinquefasciatus") ## not in the dataset
table(w$VectorSpecies %in% species)##
## FALSE TRUE
## 5000 7275 Number of reports for every country
reports <- w %>%
group_by(Country, Country_ISO) %>%
summarise(n(), diseases=length(unique(VBD_AS_Full)), vectorSP=length(unique(VectorSpecies)))## `summarise()` has grouped output by 'Country'. You can override using the
## `.groups` argument.5.1 Reading the World map
wm <- st_read("TM_WORLD_BORDERS_SIMPL-0.3.shp")## Reading layer `TM_WORLD_BORDERS_SIMPL-0.3' from data source
## `C:\Users\alfredo.acosta\OneDrive - SVA\LORA\Working example\vectors\TM_WORLD_BORDERS_SIMPL-0.3.shp'
## using driver `ESRI Shapefile'
## Simple feature collection with 246 features and 11 fields
## Geometry type: MULTIPOLYGON
## Dimension: XY
## Bounding box: xmin: -180 ymin: -90 xmax: 180 ymax: 83.57027
## Geodetic CRS: WGS 845.2 Number of reports on vectors (pop-up showing the number of on the map
# WORLD MAP ----
# Update the number of outbreaks on the map
wm$reports <- reports$`n()`[match(wm$ISO2, reports$Country_ISO)]
wm$diseases <- reports$diseases[match(wm$ISO2, reports$Country_ISO)]
wm$vectors <- reports$vectorSP[match(wm$ISO2, reports$Country_ISO)]
str(wm$reports)## int [1:246] 4 15 NA 11 6 NA NA 8 250 NA ...# Maps of outbreaks
pal <- colorNumeric(
palette = "Spectral",
domain = wm$reports,
na.color = "white"
)
# Maps of cases ----
pal <- colorNumeric(
palette = "Spectral",
reverse = TRUE,
domain = wm$reports,
na.color = "white")
map <- leaflet(wm) %>%
addProviderTiles(providers$CartoDB.Positron)
mc <- map %>%
setView(lng = 25, lat = 10, zoom = 2) %>%
addPolygons(weight = 0.5,
color = ~pal(reports),
popup = ~paste("Diseases:", diseases, "<br>", "Vectors", vectors)) %>%
addLegend("bottomright", pal = pal, values = ~reports,
# title = paste("Cases",
# "<br>",
# date_to_analyse,
# "<br>",
# disease_to_analyse),
opacity = 1)
mc6 African Swine fever
reports <- w %>%
filter(VBD_Agent_subtype == "ASFV") %>%
group_by(Country, Country_ISO) %>%
summarise(n(), vector=length(unique(VectorSpecies)), vectorSP=paste(unique(VectorSpecies), collapse = ", "))## `summarise()` has grouped output by 'Country'. You can override using the
## `.groups` argument.reports## # A tibble: 7 × 5
## # Groups: Country [7]
## Country Country_ISO `n()` vector vectorSP
## <chr> <chr> <int> <int> <chr>
## 1 China CN 25 10 Culicoides homotomus, Culicoides obsole…
## 2 Malawi MW 167 1 Ornithodoros moubata s.l.
## 3 Mozambique MZ 14 2 Ornithodoros porcinus porcinus, Ornitho…
## 4 Namibia NA 1 1 Ornithodoros porcinus
## 5 South Africa ZA 18 8 Ornithodoros waterbergensis, Ornithodor…
## 6 Tanzania TZ 11 2 Ornithodoros moubata s.l., Ornithodoros…
## 7 Zimbabwe ZW 3 1 Ornithodoros porcinus6.1 Map Number of reports on vectors (pop-up showing the name of on the map)
# WORLD MAP ----
# Update the number of outbreaks on the map
wm$reports <- reports$`n()`[match(wm$ISO2, reports$Country_ISO)]
wm$vector <- reports$vector[match(wm$ISO2, reports$Country_ISO)]
wm$vectorSP <- reports$vectorSP[match(wm$ISO2, reports$Country_ISO)]
str(wm$reports)## int [1:246] NA NA NA NA NA NA NA NA NA NA ...# Maps of outbreaks
pal <- colorNumeric(
palette = "Spectral",
domain = wm$reports,
na.color = "white"
)
# Maps of cases ----
pal <- colorNumeric(
palette = "Spectral",
reverse = TRUE,
domain = wm$reports,
na.color = "white")
map <- leaflet(wm) %>%
addProviderTiles(providers$CartoDB.Positron)
mc <- map %>%
setView(lng = 25, lat = 10, zoom = 2) %>%
addPolygons(weight = 0.5,
color = ~pal(reports),
popup = ~paste("N vectors:", vector, "<br>", "Names", vectorSP)) %>%
addLegend("bottomright", pal = pal, values = ~reports,
# title = paste("Cases",
# "<br>",
# date_to_analyse,
# "<br>",
# disease_to_analyse),
opacity = 1)
mc7 West nile virus
reports <- w %>%
filter(VBD_Agent_subtype == "WNV") %>%
group_by(Country, Country_ISO) %>%
summarise(n(), vector=length(unique(VectorSpecies)), vectorSP=paste(unique(VectorSpecies), collapse = ", "))## `summarise()` has grouped output by 'Country'. You can override using the
## `.groups` argument.reports## # A tibble: 32 × 5
## # Groups: Country [32]
## Country Country_ISO `n()` vector vectorSP
## <chr> <chr> <int> <int> <chr>
## 1 Algeria DZ 3 3 Culex perexiguus, Aedes caspius, Cul…
## 2 Austria AT 2 1 Culex pipiens/torrentium
## 3 Bulgaria BG 1 1 Culex pipiens
## 4 Canada CA 39 20 Culex pipiens/restuans, Culex salina…
## 5 China CN 9 9 Culex tritaeniorhynchus, Anopheles s…
## 6 Cyprus CY 30 3 Culex pipiens, Aedes detritus, Culex…
## 7 Czech Republic CZ 17 9 Aedes vexans, Aedes cinereus, Aedes …
## 8 France FR 1 1 Ornithodoros maritimus
## 9 Germany DE 14 8 Aedes cinereus/geminus, Aedes japoni…
## 10 Greece EL 125 4 Culex pipiens, Culex pipiens s.l., A…
## # ℹ 22 more rows7.1 Map Number of reports on vectors (pop-up showing the name of on the map)
# WORLD MAP ----
# Update the number of outbreaks on the map
wm$reports <- reports$`n()`[match(wm$ISO2, reports$Country_ISO)]
wm$vector <- reports$vector[match(wm$ISO2, reports$Country_ISO)]
wm$vectorSP <- reports$vectorSP[match(wm$ISO2, reports$Country_ISO)]
str(wm$reports)## int [1:246] NA 3 NA NA NA NA NA NA NA NA ...# Maps of outbreaks
pal <- colorNumeric(
palette = "Spectral",
domain = wm$reports,
na.color = "white"
)
# Maps of cases ----
pal <- colorNumeric(
palette = "Spectral",
reverse = TRUE,
domain = wm$reports,
na.color = "white")
map <- leaflet(wm) %>%
addProviderTiles(providers$CartoDB.Positron)
mc <- map %>%
setView(lng = 25, lat = 10, zoom = 2) %>%
addPolygons(weight = 0.5,
color = ~pal(reports),
popup = ~paste("N vectors:", vector, "<br>", "Names", vectorSP)) %>%
addLegend("bottomright", pal = pal, values = ~reports,
# title = paste("Cases",
# "<br>",
# date_to_analyse,
# "<br>",
# disease_to_analyse),
opacity = 1)
mc8 BTV
reports <- w %>%
filter(VBD_Agent_subtype == "BTV") %>%
group_by(Country, Country_ISO) %>%
summarise(n(), vector=length(unique(VectorSpecies)), vectorSP=paste(unique(VectorSpecies), collapse = ", "))## `summarise()` has grouped output by 'Country'. You can override using the
## `.groups` argument.reports## # A tibble: 12 × 5
## # Groups: Country [11]
## Country Country_ISO `n()` vector vectorSP
## <chr> <chr> <int> <int> <chr>
## 1 Belgium BE 34 6 Culicoides obsoletus complex, Culicoide…
## 2 China CN 33 15 Culicoides homotomus, Culicoides obsole…
## 3 France FR 1 1 Culicoides imicola
## 4 Germany DE 5 2 Culicoides obsoletus group, Culicoides …
## 5 Italy IT 110 12 Culicoides imicola, Culicoides newstead…
## 6 Italy <NA> 7 6 Culicoides imicola, Culicoides obsoletu…
## 7 Japan JP 12 12 Culicoides oxystoma, Culicoides tainanu…
## 8 Netherlands <NA> 9 5 Culicoides obsoletus complex, Culicoide…
## 9 Romania RO 13 3 Culicoides obsoletus complex, Culicoide…
## 10 Russia RU 2 2 Culicoides obsoletus complex, Culicoide…
## 11 Thailand TH 15 5 Culicoides peregrinus, Culicoides orien…
## 12 USA US 25 6 Culicoides crepuscularis, Culicoides de…8.1 Map Number of reports on vectors (pop-up showing the name of on the map)
# WORLD MAP ----
# Update the number of outbreaks on the map
wm$reports <- reports$`n()`[match(wm$ISO2, reports$Country_ISO)]
wm$vector <- reports$vector[match(wm$ISO2, reports$Country_ISO)]
wm$vectorSP <- reports$vectorSP[match(wm$ISO2, reports$Country_ISO)]
str(wm$reports)## int [1:246] NA NA NA NA NA NA NA NA NA NA ...# Maps of outbreaks
pal <- colorNumeric(
palette = "Spectral",
domain = wm$reports,
na.color = "white"
)
# Maps of cases ----
pal <- colorNumeric(
palette = "Spectral",
reverse = TRUE,
domain = wm$reports,
na.color = "white")
map <- leaflet(wm) %>%
addProviderTiles(providers$CartoDB.Positron)
mc <- map %>%
setView(lng = 25, lat = 10, zoom = 2) %>%
addPolygons(weight = 0.5,
color = ~pal(reports),
popup = ~paste("N vectors:", vector, "<br>", "Names", vectorSP)) %>%
addLegend("bottomright", pal = pal, values = ~reports,
# title = paste("Cases",
# "<br>",
# date_to_analyse,
# "<br>",
# disease_to_analyse),
opacity = 1)
mc9 MIR Mininum infection rates
9.1 Selection of pririotized diseases
# ASF African Swine Fever
# CCHF Crimean-Congo Haemorrhagic fever
# EHD Epizootic Haemorrhagic Disease
# EE Equine Encephalosis
# *** HPAI Highly Pathogenic Avian Influenza
# JE Japanese Encephalitis
# *** LSD Lumpy Skin Disease
# *** Rab Rabies
# RVF Rift Valley Fever
# WNF West Nile Fever
#
head(w)## # A tibble: 6 × 42
## ID First_Author Title year Country `Region/State` `City/County` Latitude
## <chr> <chr> <chr> <dbl> <chr> <chr> <chr> <chr>
## 1 2 Li Invest… 2017 China Yunnan provin… <NA> "Sampli…
## 2 2 Li Invest… 2017 China Yunnan provin… <NA> "Sampli…
## 3 2 Li Invest… 2017 China Yunnan provin… <NA> "Sampli…
## 4 2 Li Invest… 2017 China Yunnan provin… <NA> "Sampli…
## 5 2 Li Invest… 2017 China Yunnan provin… <NA> "Sampli…
## 6 2 Li Invest… 2017 China Yunnan provin… <NA> "Sampli…
## # ℹ 34 more variables: Longitude <dbl>, Continent <chr>, Year_Start <chr>,
## # Year_End <chr>, Month_Start <chr>, Month_End <chr>,
## # Continuous_or_annually <chr>, SamplingMethod <chr>, LifeStage <chr>,
## # VectorGroup <chr>, VectorSpecies <chr>, VectorSpeciesOld <chr>,
## # fedStatus <chr>, Host <chr>, anMethCode <chr>, MethodCategory <chr>,
## # `NÂSpecimensÂTested` <dbl>, NPoolsTested <dbl>, Pool_size <chr>,
## # `Positive/Negative` <chr>, NPoolspositive <chr>, VBD_Agent <chr>, …# Which abreviattion correspond to the disease
w %>%
group_by(w$VBD_Agent_subtype, w$VBD_AS_Full) %>%
summarise(n())## `summarise()` has grouped output by 'w$VBD_Agent_subtype'. You can override
## using the `.groups` argument.## # A tibble: 27 × 3
## # Groups: w$VBD_Agent_subtype [27]
## `w$VBD_Agent_subtype` `w$VBD_AS_Full` `n()`
## <chr> <chr> <int>
## 1 AHFV Alkhurma haemorrhagic fever virus 13
## 2 AHSV African horse sickness virus 27
## 3 AKAV Akabane virus 21
## 4 ASFV African swine fever virus 239
## 5 BTV Bluetongue virus 266
## 6 CCHFV Crimean-Congo haemorrhagic fever virus 637
## 7 CVV Cache Valley virus 120
## 8 CanL Leishmania infantum 567
## 9 Cowdr Ehrlichia ruminantium 174
## 10 EEEV Eastern equine encephalitis virus 118
## # ℹ 17 more rowsdi <- c("ASFV","BTV","CCHFV", "EHDV", "EEV", "JEV", "RVFV", "WNV")9.2 Options to filter
table(w$fedStatus)##
## Fed Fed and unfed
## 307 227
## Fed or unknown Gravid
## 22 30
## Gravid or unknown Gravid, semigravid, nongravid
## 8 1
## Parous Parous or gravid
## 7 9
## Unfed
## 571table(w$LifeStage)##
## Adult Eggs
## 1770 1
## Eggs, larvae, pupae reared to adult Female
## 37 2887
## Larvae Larvae, adult
## 67 62
## Larvae, nymph Larvae, nymph, adult
## 9 77
## Male Nymph
## 129 115
## Nymph, adult
## 2359.3 Filtering criteria for Mosquitoes, Bitting midges and Sand flies (127)
a <- w %>%
filter(MIR > 0) %>%
# filter(VBD_Agent_subtype %in% di) %>%
filter(fedStatus == "Unfed" | fedStatus == "Gravid") %>%
filter(VectorGroup == "Mosquitoes" | VectorGroup == "Biting midges" | VectorGroup == "Sand flies") %>%
filter(LifeStage == "Female")9.4 Filter criteria for Ticks (27)
b <- w %>%
filter(MIR > 0) %>%
filter(fedStatus == "Unfed" | fedStatus == "Gravid") %>%
filter(VectorGroup == "Ticks")9.5 Number of MIR values (Checking filter)
# Minimum infection rates
# After applying the filtering criteria on the feeding status and life stage, 42 MIR values were
# found or calculated for mosquitoes, 67 for sand flies, 27 for ticks, and 18 for biting midges.
# Records including MIR values are visualized in a boxplot grouped by vector group (Figure 4).
# Details per arthropod species are provided in Appendix F.
c <- rbind(a,b)
c %>% group_by(VectorGroup) %>%
summarise(n())## # A tibble: 4 × 2
## VectorGroup `n()`
## <chr> <int>
## 1 Biting midges 18
## 2 Mosquitoes 42
## 3 Sand flies 67
## 4 Ticks 2710 MIR Table
c <- rbind(a,b)
datatable(c %>%
filter(VBD_Agent_subtype %in% di) %>%
group_by(VBD_AS_Full, VectorGroup) %>%
summarise(obs = n(),Min=round(min(MIR),2), Median=round(median(MIR),2), Max=round(max(MIR),2)))## `summarise()` has grouped output by 'VBD_AS_Full'. You can override using the
## `.groups` argument.10.1 MIR considerig disease, vector group and species
datatable(c %>%
filter(VBD_Agent_subtype %in% di) %>%
group_by(VBD_AS_Full, VectorGroup, VectorSpecies) %>%
summarise(obs = n(),Min=round(min(MIR),2), Median=round(median(MIR),2), Max=round(max(MIR),2)))## `summarise()` has grouped output by 'VBD_AS_Full', 'VectorGroup'. You can
## override using the `.groups` argument.11 Boxplot of MIR - Disease
c %>%
filter(VBD_Agent_subtype %in% di) %>%
group_by(VBD_AS_Full, VectorGroup) %>%
ggplot(aes(MIR, VBD_AS_Full)) +
geom_boxplot()+
labs(y = "Disease", x= "MIR %o")
11.1 Boxplot of MIR - Disease/VectorGroup
c %>%
filter(VBD_Agent_subtype %in% di) %>%
group_by(VBD_AS_Full, VectorGroup, VectorSpecies) %>%
ggplot(aes(MIR, color=VBD_AS_Full, VectorGroup)) +
geom_boxplot()+
facet_grid(cols=vars(VBD_AS_Full), scales = "free")+
theme(legend.position="none")+
labs(y = "Disease", x= "MIR %o")
11.2 Boxplot of MIR - Disease/Species
c %>%
filter(VBD_Agent_subtype %in% di) %>%
group_by(VBD_AS_Full, VectorGroup, VectorSpecies) %>%
ggplot(aes(MIR, color=VBD_AS_Full, VectorSpecies)) +
geom_boxplot()+
facet_grid(cols=vars(VBD_AS_Full), scales = "free")+
theme(legend.position="none")+
labs(y = "Disease", x= "MIR %o")